The film takes place in Boston. Irish Mob boss Francis "Frank" Costello (Nicholson) plants Colin Sullivan (Damon) as a mole within the Massachusetts State Police; the two characters are loosely based on famous gangster Whitey Bulger and corrupt FBI agent John Connolly, who grew up with Bulger.[3][4] Simultaneously, the police assign undercover state trooper William "Billy" Costigan (Leonardo DiCaprio) to infiltrate Costello's crew. When both sides realize the situation, Sullivan and Costigan each attempt to discover the other's identity before they are found out.

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As a child, Colin Sullivan is introduced to organized crime by Irish-American mobster Frank Costello in the Irish neighborhood of South Boston. Over the years, Costello grooms him to become a mole inside the Massachusetts State Police. Sullivan is accepted into the Special Investigations Unit, which focuses on organized crime.

Before graduating from the state police academy, Billy Costigan is recruited by Captain Queenan and Staff Sergeant Dignam to go undercover, as his family ties to organized crime make him a perfect infiltrator. He drops out of the academy and serves time in prison on a fake assault charge to increase his credibility.

Each man infiltrates his respective target organization. Sullivan begins a romance with police psychiatrist Madolyn Madden. Costigan sees her as a condition of his probation, and they begin a relationship, too. After Costello escapes a sting operation, each mole becomes aware of the other's existence. Sullivan is told to find the "rat" and asks Costello for information to identify the informer.

Costigan follows Costello into a porn theater, where Costello gives Sullivan an envelope containing personal information on his crew members. Costigan chases Sullivan through Chinatown. When it is over, neither man knows the other's identity. Sullivan has Queenan tailed to a meeting with Costigan on the roof of a warehouse. Queenan orders Costigan to flee while he confronts Costello's men alone. Queenan is tossed off the roof by Costello's henchmen and takes a deadly plunge. When they exit, Costigan pretends he has come to join them. During their escape from the police, crew member Delahunt is shot, and he later dies. Television news states that Delahunt had been an undercover cop, working for the Boston Police Department, but Costello does not believe the story. With Queenan's absence, Dignam resigns rather than work with Sullivan, who he suspects is the mole.

Using Queenan's phone, Sullivan reaches Costigan, who refuses to abort his mission. Sullivan learns from Queenan's diary of Costello's role as an informant for the FBI, causing him to worry about his own identity being revealed. With Costigan's help, Costello is traced to a cocaine drop-off, where a gunfight erupts between Costello's crew and the police. Most of the crew are killed. Costello, confronted by Sullivan, admits he is an FBI informant. Costello tries to shoot Sullivan, but Sullivan shoots him multiple times. With Costello dead, Sullivan is applauded the next day by everyone on the force. In good faith, Costigan comes to Sullivan for restoration of his true identity and to be paid for his work, but notices the envelope from Costello on Sullivan's desk and flees, finally realizing Sullivan is the enemy. Fearing retaliation, Sullivan erases Costigan's records from the police computer system.

Sullivan is unaware that Madolyn had an affair with Costigan when she tells Sullivan that she is pregnant. Later, Sullivan finds her listening to a CD from Costigan containing incriminating recorded conversations between Costello and Sullivan. Sullivan unsuccessfully attempts to assuage her suspicions. He contacts Costigan, who reveals that Costello had recorded each of their conversations, and his attorney arranged for Costigan to take possession of the recordings, and Costigan intends to implicate Sullivan. The two agree to meet at the building where Queenan was killed.

On the roof, Costigan catches Sullivan off-guard and handcuffs him. As Costigan had secretly arranged, Trooper Brown appears on the roof as well. Shocked, Brown draws his gun on Costigan, who attempts to justify his actions by exposing Sullivan as Costello's mole. Costigan asks Brown why Dignam did not accompany him as Costigan had requested, but Brown does not answer. Costigan leads Sullivan, his hostage, to the elevator. When it reaches the ground floor, Trooper Barrigan shoots Costigan in the head, then shoots Brown, and afterward reveals to Sullivan that Costello had more than one mole in the police. Sullivan shoots and kills Barrigan. At state police headquarters, Sullivan identifies Barrigan as the mole and has Costigan posthumously given the Medal of Merit.

At Costigan's funeral, Sullivan notices that Madolyn is tearful. As they leave the gravesite, Sullivan attempts to talk to her, but she ignores him. When Sullivan returns to his apartment, he is ambushed by Dignam, who shoots and kills him as he enters.

In March 2004, United Press International announced that Scorsese would be remaking Infernal Affairs and setting it in Boston, and Leonardo DiCaprio and Brad Pitt were slated to star.[9] Pitt, tentatively scheduled to play Sullivan, later declined to play the role, saying a younger actor should play the part; he decided to produce the film instead.[8] Scorsese's associate Kenneth Lonergan suggested Matt Damon, who grew up in Boston, for the part of Sullivan, and Scorsese asked Jack Nicholson to play Costello.[4]

Nicholson, however, wanted the film to have "something a little more" than the usual gangster film, and screenwriter Monahan came up with the idea of basing the Costello character on the famous Irish-American gangster Whitey Bulger. This gave the screenplay an element of realism – and also an element of dangerous uncertainty, because of the wide-ranging carte blanche the FBI gave Bulger in exchange for revealing information about fellow gangsters.[4] A technical consultant on the film was Tom Duffy, who had served three decades on the Boston Police Department, particularly as an undercover detective investigating the Irish mob.[10][11]

The film got the official greenlight from Warners in early 2005, and began shooting in the spring of 2005.[7] Although some of the film was shot on location in Boston, for budgetary and logistical reasons many scenes, interiors in particular, were shot in locations and sets in New York City, which had tax incentives for filmmakers that Boston at the time did not.[4][12]

Film critic Stanley Kauffmann describes a major theme of The Departed as one of the oldest in drama – the concept of identity – and how it "affects one's actions, emotions, self-assurance and even dreams."[13]

The father-son relationship is a motif throughout the film. Costello acts as a father figure to both Sullivan and Costigan, while Queenan acts as Costello's foil in the role of father figure. Sullivan refers to Costello as "Dad" whenever he calls to inform him of police activities.

In the final scene, a rat is seen on Sullivan's window ledge. Scorsese acknowledges that while it is not meant to be taken literally, it somewhat symbolizes the "quest for the rat" in the film and the strong sense of distrust among the characters, much like post-9/11 America. The window view behind the rat is a nod to gangster films like Scarface (1932), White Heat (1949), and Little Caesar (1931).[14]

Throughout the film, Scorsese uses an "X" motif to foreshadow death in a manner similar to Howard Hawks' classic film Scarface (1932). Examples include (but are not limited to) shots of cross-beam supports in an airport walkway when Costigan is phoning Sgt. Dignam, the taped windows of the building Queenan enters before being thrown to his death, behind Costigan's head in the elevator before he's shot, and the carpeted hallway floor when Sullivan returns to his apartment at the film's end.[15]

The Departed grossed $132.4 million in the United States and Canada and $159 million in other territories for a total gross of $291.5 million, against a production budget of $90 million.[1]

The film grossed $26.9 million in its opening weekend, becoming the third Scorsese film to debut at number one.[16] In the following three weeks the film grossed $19 million, $13.5 million and $9.8 million, finishing second at the box office each time, before grossing $7.7 million and dropping to 5th in its fifth week.[17]

On Rotten Tomatoes, the film has an approval rating of 91% based on 272 reviews, with an average rating of 8.2/10. The website's critical consensus reads, "Featuring outstanding work from an excellent cast, The Departed is a thoroughly engrossing gangster drama with the gritty authenticity and soupy morality we come to expect from Martin Scorsese."[18] On Metacritic, the film has a score of 85 out of 100, based on 39 critics, indicating "universal acclaim".[19] On CinemaScore, audiences gave the film an average grade of "A–" on an A+ to F scale.[20]

Entertainment Weekly put it on its end-of-the-decade "best of" list, saying: "If they're lucky, directors make one classic film in their career. Martin Scorsese has one per decade (Taxi Driver in the '70s, Raging Bull in the '80s, Goodfellas in the '90s). His 2006 Irish Mafia masterpiece kept the streak alive."[21]

Online critic James Berardinelli awarded the film four stars out of four, praising it as "an American epic tragedy." He went on to claim that the film deserves to be ranked alongside Scorsese's past successes, including Taxi Driver, Raging Bull and Goodfellas.[22]

Andrew Lau, the co-director of Infernal Affairs, who was interviewed by Hong Kong newspaper Apple Daily, said: "Of course I think the version I made is better, but the Hollywood version is pretty good too. [Scorsese] made the Hollywood version more attuned to American culture." Andy Lau,[23] one of the main actors in Infernal Affairs, when asked how the movie compares to the original, said: "The Departed was too long and it felt as if Hollywood had combined all three Infernal Affairs movies together."[24] Lau pointed out that the remake featured some of the "golden quotes" of the original but had much more profanity. He ultimately rated The Departed 8/10 and said that the Hollywood remake is worth a view, though according to Lau's spokeswoman Alice Tam, he felt that the combination of the two female characters into one in The Departed was not as good as the original storyline.[25]

A few critics were disappointed in the film, including J. Hoberman of the Village Voice, who wrote: "Overwrought as The Departed may be, it's nothing that wouldn't have been cured by losing Jack [Nicholson] (and maybe half an hour). Too bad the bottom line meant Scorsese had to sell that hambone Mephistopheles his soul."[26]

The film marked the first time Scorsese won an Oscar after six previous losses.[30] Many felt that he deserved it years earlier for prior efforts.[31] Some have even gone further, calling it a Lifetime Achievement Award for a lesser film.[32] Scorsese himself joked that he won because: "This is the first movie I've done with a plot."[33] While accepting the award, Scorsese stated that "I just want to say, too, that so many people over the years have been wishing this for me, strangers, you know. I go walking in the street people say something to me, I go in a doctor's office, I go in a...whatever...elevators, people are saying, "You should win one, you should win one." I go for an x-ray, "You should win one." And I'm saying, "Thank you." And then friends of mine over the years and friends who are here tonight are wishing this for me and my family. I thank you. This is for you."

The Departed was released by Warner Brothers on DVD in 2007. The film is available in a single-disc full screen (1.33:1), single-disc widescreen (2.40:1) edition, and 2-disc special edition. The second disc contains deleted scenes; a feature about the influence of New York’s Little Italy on Scorsese; a Turner Classic Movies profile; and a 21-minute documentary titled Stranger Than Fiction: The True Story of Whitey Bulger, Southie and The Departed[35] about the crimes that influenced Scorsese in creating the film, including the story of James "Whitey" Bulger, upon whom Jack Nicholson's character is based.[36]

The Region 1 version has three available audio tracks: English, Spanish, and French (all of which are in Dolby Digital 5.1), and three subtitle tracks (English, Spanish, French). The film was released on HD DVD and Blu-ray at the same time as the standard-definition DVD. The 2-Disc Special Edition was packaged in a Limited Edition Steelbook. It marked the first time that an Oscar-winning Best Picture was released to the home video market in DVD format only, as VHS was totally phased out by the start of 2006.

There were two albums released for The Departed, one presenting the original score composed for the film by Howard Shore, and the other featuring earlier recordings, mostly pop/rock songs, which were used on the soundtrack.